A. G. Clark

Inference of selective sweep parameters through supervised learning

This paper develops a machine learning method to infer selective sweep parameters from genetic data, accurately classifying sweep types and estimating selection coefficients.

Octopaminergic/tyraminergic Tdc2 neurons regulate biased sperm usage in female Drosophila melanogaster

This study shows that Tdc2 neurons in Drosophila melanogaster regulate biased sperm usage by females, with inhibition increasing first-male progeny proportion.

Three recent sex chromosome-to-autosome fusions in a Drosophila virilis strain with high satellite content

This paper describes three recent sex chromosome-to-autosome fusions in a Drosophila virilis strain, linking satellite DNA abundance to increased genome instability and karyotype variability.

Fitness effects of CRISPR endonucleases in Drosophila melanogaster populations

This study evaluates fitness costs of CRISPR/Cas9 in Drosophila by tracking allele frequencies of transgenic constructs, finding moderate off-target costs but no direct Cas9 costs, with Cas9HF1 minimizing off-target effects.

Copy number evolution in simple and complex tandem repeats across the C57BL/6 and C57BL/10 inbred mouse lines

The paper estimates copy number change rates in tandem repeats across mouse lines over generations, finding stability in CAG repeats and variation in other repeats.

Migration Restores Hybrid Incompatibility Driven By Mitochondrial-Nuclear Sexual Conflict

The paper uses simulations to study how mitochondrial-nuclear sexual conflict affects hybrid incompatibility and population dynamics under different migration scenarios.

Differences in post-mating transcriptional responses between conspecific and heterospecific matings in Drosophila

The paper examines post-mating transcriptome responses in Drosophila females mated with conspecific and heterospecific males, finding that heterospecific mating induces stress and immune-related gene expression.

Inference of sexual selection from pairwise contests

The paper applies the Bradley-Terry model to Drosophila mate-choice experiments to infer sexual selection by quantifying contestant merits and predicting contest outcomes.

Mitochondrial-Y chromosome epistasis in Drosophila melanogaster

This study examines mitochondrial-Y chromosome epistasis in Drosophila melanogaster by analyzing longevity and gene expression across isogenic strains with different mitochondrial and Y chromosome origins.

Suppression gene drive in continuous space can result in unstable persistence of both drive and wild-type alleles

This study shows that suppression gene drives in spatial models can lead to unstable persistence of both drive and wild-type alleles due to chasing dynamics.

Allele frequency dynamics in a pedigreed natural population

This study uses pedigree and genomic data from Florida Scrub-Jays to analyze how genetic drift, selection, and gene flow influence allele frequency changes over time.

Maximum likelihood estimation of fitness components in experimental evolution

The paper develops a maximum likelihood framework to estimate fitness components in experimental evolution using Drosophila melanogaster data, finding reduced mating preference and viability for a yellow allele.

Sexual Conflict through Mother’s Curse and Father’s Curse

This study examines how genetic transmission asymmetries cause and resolve sexual conflicts through Mothers Curse and Fathers Curse mechanisms using analytical models and simulations.

Genomic responses to selection for tame/aggressive behaviors in the silver fox (Vulpes vulpes)

The paper identifies differentially expressed genes and SNPs associated with tame and aggressive behaviors in silver foxes.

Selection constrains high rates of satellite DNA mutation in Daphnia pulex

This study quantifies mutation rates and selective pressures on satellite DNA in Daphnia pulex, showing high mutation rates and evidence of purifying selection in non-MA population isolates.

Deconstructing isolation-by-distance: the genomic consequences of limited dispersal

The paper investigates how limited dispersal in Florida Scrub-Jays shapes fine-scale genetic structure, showing stronger isolation-by-distance in males due to sex-specific dispersal patterns.

Evolutionary dynamics of male reproductive genes in the Drosophila virilis subgroup

The paper examines the evolutionary dynamics of male reproductive genes in Drosophila virilis subgroup species, identifying SFPs under strong selection and linked to reproductive incompatibilities.